Highways1

Let us set some global options for all code chunks in this document.

knitr::opts_chunk$set(
  message = FALSE,    # Disable messages printed by R code chunks
  warning = FALSE,    # Disable warnings printed by R code chunks
  echo = TRUE,        # Show R code within code chunks in output
  include = TRUE,     # Include both R code and its results in output
  eval = TRUE,       # Evaluate R code chunks
  cache = FALSE,       # Enable caching of R code chunks for faster rendering
  fig.align = "center",
  out.width = "100%",
  retina = 2,
  error = TRUE,
  collapse = TRUE
)
rm(list = ls())
set.seed(1982)

1 Preprocessing

Let us now load some required libraries.

# Load required libraries

# inla.upgrade(testing = TRUE)
# remotes::install_github("inlabru-org/inlabru", ref = "devel")
# remotes::install_github("davidbolin/rspde", ref = "devel")
# remotes::install_github("davidbolin/metricgraph", ref = "devel")
# remotes::install_github("davidbolin/ngme2", ref = "devel")

library(INLA)
#inla.setOption(num.threads = 7)
library(inlabru)
library(rSPDE)
library(MetricGraph)
library(ngme2)

library(plotly)
library(dplyr)

library(sf)

library(here)

library(shiny)
library(bslib)
library(dplyr)
library(ggplot2)
library(ggExtra)

penguins_csv <- "https://raw.githubusercontent.com/jcheng5/simplepenguins.R/main/penguins.csv"

df <- readr::read_csv(penguins_csv)
# Find subset of columns that are suitable for scatter plot
df_num <- df |> select(where(is.numeric), -Year)

ui <- page_sidebar(
  sidebar = sidebar(
    varSelectInput("xvar", "X variable", df_num, selected = "Bill Length (mm)"),
    varSelectInput("yvar", "Y variable", df_num, selected = "Bill Depth (mm)"),
    checkboxGroupInput(
      "species", "Filter by species",
      choices = unique(df$Species), 
      selected = unique(df$Species)
    ),
    hr(), # Add a horizontal rule
    checkboxInput("by_species", "Show species", TRUE),
    checkboxInput("show_margins", "Show marginal plots", TRUE),
    checkboxInput("smooth", "Add smoother"),
  ),
  plotOutput("scatter")
)

server <- function(input, output, session) {
  subsetted <- reactive({
    req(input$species)
    df |> filter(Species %in% input$species)
  })

  output$scatter <- renderPlot({
    p <- ggplot(subsetted(), aes(!!input$xvar, !!input$yvar)) + list(
      theme(legend.position = "bottom"),
      if (input$by_species) aes(color = Species),
      geom_point(),
      if (input$smooth) geom_smooth()
    )

    if (input$show_margins) {
      margin_type <- if (input$by_species) "density" else "histogram"
      p <- ggExtra::ggMarginal(p, type = margin_type, margins = "both",
        size = 8, groupColour = input$by_species, groupFill = input$by_species)
    }

    p
  }, res = 100)
}

shinyApp(ui, server)

Shiny applications not supported in static R Markdown documents